cdccovidview

Weekly Surveillance Summary of U.S. COVID-19 Activity

Description

The U.S. Centers for Disease Control provides weekly summary and interpretation of key indicators that have been adapted to track the COVID-19 pandemic in the United States. Tools are provided to retrive data from both COVIDView (https://www.cdc.gov/coronavirus/2019-ncov/covid-data/covidview/index.html) and COVID-NET (https://gis.cdc.gov/grasp/COVIDNet/COVID19_3.html).

What’s Inside The Tin

The following functions are implemented:

• about: Display information about the data source
• age_groups: Return age groups used in the surveillance
• available_seasons: Show available seasons
• has_bom: Tests whether a raw httr response or character vector has a byte order mark (BOM)
• laboratory_confirmed_hospitalizations: Retrieve Laboratory-Confirmed COVID-19-Associated Hospitalizations
• mmwr_week_to_date: Convert an MMWR year+week or year+week+day to a Date object
• mmwr_week: Convert a Date to an MMWR day+week+year
• mmwr_weekday: Convert a Date to an MMWR weekday
• mmwrid_map: MMWR ID to Calendar Mappings
• sans_bom: Remove byte order mark (BOM) from httr::response object or character vector
• surveillance_areas: Show network & network catchments

Installation

remotes::install_git("https://git.rud.is/hrbrmstr/cdccovidview.git")
# or
remotes::install_git("https://git.sr.ht/~hrbrmstr/cdccovidview")
# or
remotes::install_gitlab("hrbrmstr/cdccovidview")
# or
remotes::install_bitbucket("hrbrmstr/cdccovidview")

NOTE: To use the ‘remotes’ install options you will need to have the {remotes} package installed.

Usage

library(cdccovidview)

# current version
packageVersion("cdccovidview")
## [1] '0.1.0'

library(cdccovidview)
library(hrbrthemes)
library(tidyverse)

hosp <- laboratory_confirmed_hospitalizations()

c(
  "0-4 yr", "5-17 yr", "18-49 yr", "50-64 yr", "65+ yr", "65-74 yr", "75-84 yr", "85+"
) -> age_f

mutate(hosp, start = mmwr_week_to_date(mmwr_year, mmwr_week)) %>% 
  filter(!is.na(weekly_rate)) %>% 
  filter(catchment == "Entire Network") %>% 
  select(start, network, age_category, weekly_rate) %>%  
  filter(age_category != "Overall") %>% 
  mutate(age_category = factor(age_category, levels = age_f)) %>% 
  ggplot() +
  geom_line(
    aes(start, weekly_rate)
  ) +
  scale_x_date(
    date_breaks = "2 weeks", date_labels = "%b\n%d"
  ) +
  facet_grid(network~age_category) +
  labs(
    x = NULL, y = "Rates per 100,000 pop",
    title = "COVID-NET Weekly Rates by Network and Age Group",
    caption = sprintf("Source: COVID-NET: COVID-19-Associated Hospitalization Surveillance Network, Centers for Disease Control and Prevention.\n<https://gis.cdc.gov/grasp/COVIDNet/COVID19_3.html>; Accessed on %s", Sys.Date())
  ) +
  theme_ipsum_es(grid="XY")

cdccovidview Metrics

Lang	# Files	(%)	LoC	(%)	Blank lines	(%)	# Lines	(%)
R	11	0.92	200	0.85	75	0.79	136	0.82
Rmd	1	0.08	35	0.15	20	0.21	30	0.18

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.